fix: correct BindCraft settings JSON format across use cases

.gitignore

@@ -18,3 +18,4 @@ templates/
 params/
 repo/
 examples/
+.omc/

Dockerfile

@@ -5,25 +5,53 @@
 #   1. builder  – installs all conda/pip dependencies
 #   2. runtime  – minimal image with only what's needed to run
 #
-# Build:
+# Build (without proxy):
 #   docker build -t bindcraft-mcp .
 #
+# Build (with proxy - recommended for China):
+#   docker build --build-arg HTTP_PROXY=http://host.docker.internal:7890 \
+#                --build-arg HTTPS_PROXY=http://host.docker.internal:7890 \
+#                -t bindcraft-mcp .
+#
 # Run (GPU):
 #   docker run --gpus all -it bindcraft-mcp
 #
 # Run (CPU-only):
 #   docker run -it bindcraft-mcp
 ###############################################################################
 
+# Proxy configuration (pass via --build-arg)
+ARG HTTP_PROXY
+ARG HTTPS_PROXY
+ARG NO_PROXY
+
 # ---------- Stage 1: builder ----------
 FROM continuumio/miniconda3:24.7.1-0 AS builder
 
+# Re-declare ARGs for this stage
+ARG HTTP_PROXY
+ARG HTTPS_PROXY
+ARG NO_PROXY
+
+# Set environment variables for proxy in builder stage
+ENV HTTP_PROXY=${HTTP_PROXY}
+ENV HTTPS_PROXY=${HTTPS_PROXY}
+ENV NO_PROXY=${NO_PROXY}
+ENV http_proxy=${HTTP_PROXY}
+ENV https_proxy=${HTTPS_PROXY}
+ENV no_proxy=${NO_PROXY}
+
 RUN apt-get update && apt-get install -y \
     git gcc g++ wget \
     && rm -rf /var/lib/apt/lists/*
 
 WORKDIR /app
 
+# Configure conda to use USTC mirror (China)
+RUN mkdir -p /root/.conda && \
+    printf 'channels:\n  - https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge/\nshow_channel_urls: true\n' > /root/.condarc && \
+    conda clean -i
+
 # Create conda environment with all dependencies
 RUN conda create -p /env python=3.10 -y
 
@@ -38,14 +66,15 @@ RUN conda install -p /env \
     chex dm-haiku 'flax<0.10.0' dm-tree joblib ml-collections immutabledict optax \
     -c conda-forge -y
 
-# Install JAX with CUDA 12 support for GPU acceleration
-RUN /env/bin/pip install --no-cache-dir 'jax[cuda12]>=0.4,<=0.6.0'
+# Configure pip to use USTC mirror and install JAX with CUDA 12 support
+RUN /env/bin/pip config set global.index-url https://mirrors.ustc.edu.cn/pypi/simple && \
+    /env/bin/pip install --no-cache-dir 'jax[cuda12]>=0.4,<=0.6.0'
 
 # Install PyRosetta (may fail without license – non-fatal)
 RUN conda install -p /env pyrosetta pdbfixer \
     --channel https://conda.graylab.jhu.edu -c conda-forge -y 2>/dev/null || true
 
-# Install pip packages
+# Install pip packages (using USTC mirror configured above)
 RUN /env/bin/pip install --no-cache-dir fastmcp==2.13.1 loguru click
 RUN /env/bin/pip install --no-cache-dir git+https://github.com/sokrypton/ColabDesign.git --no-deps || true
 
@@ -55,6 +84,19 @@ RUN conda clean -a -y
 # ---------- Stage 2: runtime ----------
 FROM continuumio/miniconda3:24.7.1-0 AS runtime
 
+# Re-declare ARGs for this stage
+ARG HTTP_PROXY
+ARG HTTPS_PROXY
+ARG NO_PROXY
+
+# Set environment variables for proxy in runtime stage
+ENV HTTP_PROXY=${HTTP_PROXY}
+ENV HTTPS_PROXY=${HTTPS_PROXY}
+ENV NO_PROXY=${NO_PROXY}
+ENV http_proxy=${HTTP_PROXY}
+ENV https_proxy=${HTTPS_PROXY}
+ENV no_proxy=${NO_PROXY}
+
 RUN apt-get update && apt-get install -y \
     libgomp1 libgfortran5 git wget \
     && rm -rf /var/lib/apt/lists/*
@@ -118,6 +160,14 @@ ENV FONTCONFIG_PATH=/app/.fontconfig
 ENV NVIDIA_VISIBLE_DEVICES=all
 ENV NVIDIA_DRIVER_CAPABILITIES=compute,utility
 
+# Reset proxy environment variables (don't carry proxy into runtime)
+ENV HTTP_PROXY=
+ENV HTTPS_PROXY=
+ENV NO_PROXY=
+ENV http_proxy=
+ENV https_proxy=
+ENV no_proxy=
+
 # Allow any UID to resolve via NSS (fixes getpwuid KeyError for --user flag)
 RUN chmod 666 /etc/passwd
 # Create entrypoint that adds the runtime UID to /etc/passwd if missing

README.md

@@ -44,6 +44,20 @@ cd bindcraft_mcp
 # Build the Docker image
 docker build -t bindcraft_mcp:latest .
 
+# Build with proxy (recommended for users in China)
+docker build --build-arg HTTP_PROXY=http://host.docker.internal:7890 \
+             --build-arg HTTPS_PROXY=http://host.docker.internal:7890 \
+             -t bindcraft_mcp:latest .
+```
+
+**Note for users in China:** The Dockerfile is pre-configured to use USTC mirrors for both conda and pip, which significantly speeds up package downloads without requiring a proxy:
+- **Conda**: `https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge`
+- **PyPI**: `https://mirrors.ustc.edu.cn/pypi/simple`
+
+```bash
+# Build without proxy (uses USTC mirrors by default)
+docker build -t bindcraft_mcp:latest .
+
 # Register with Claude Code (runs as current user to avoid permission issues)
 claude mcp add bindcraft -- docker run -i --rm --user `id -u`:`id -g` --gpus all --ipc=host -v `pwd`:`pwd` bindcraft_mcp:latest
 ```

clean_scripts/use_case_1_quick_design.py

@@ -57,22 +57,30 @@ def generate_target_settings(
     binder_length: int = 130,
     num_designs: int = 1
 ) -> Dict[str, Any]:
-    """Generate target settings JSON for BindCraft."""
+    """Generate target settings JSON for BindCraft in correct format.
+
+    Returns settings in the format expected by run_bindcraft.py:
+    - design_path: Output directory for designed binders
+    - binder_name: Prefix name for designed binders
+    - starting_pdb: Target protein PDB structure
+    - chains: Target chain(s) to design binder against
+    - target_hotspot_residues: Residue numbers to target (comma-separated)
+    - lengths: [min_length, max_length] range for binder length
+    - number_of_final_designs: Target number of accepted designs
+    """
     target_pdb_abs = resolve_path(target_pdb)
     output_dir_abs = resolve_path(output_dir)
 
     settings = {
-        "target_pdb": target_pdb_abs,
-        "target_chains": chains,
+        "design_path": output_dir_abs,                    # NOT "output_dir"
         "binder_name": name,
-        "binder_length": binder_length,
-        "num_designs": num_designs,
-        "output_dir": output_dir_abs,
+        "starting_pdb": target_pdb_abs,                   # NOT "target_pdb"
+        "chains": chains,                                  # NOT "target_chains"
+        "target_hotspot_residues": hotspot if hotspot else "",  # NOT "hotspot"
+        "lengths": [binder_length, binder_length],        # Array format, NOT single int
+        "number_of_final_designs": num_designs            # NOT "num_designs"
     }
 
-    if hotspot:
-        settings["hotspot"] = hotspot
-
     return settings
 
 
@@ -165,14 +173,17 @@ def run_quick_design(
         settings_file = output_dir / "target_settings.json"
         save_json(target_settings, settings_file)
 
+        # Get absolute path to settings file
+        settings_file_abs = str(settings_file.resolve())
+
         # Prepare command
         filters_json = defaults["filters"] if final_config["filters_enabled"] else None
         advanced_json = defaults["advanced"]
 
         cmd = [
             sys.executable,
             str(bindcraft_path / "run_bindcraft.py"),
-            f"--settings={settings_file}",
+            f"--settings={settings_file_abs}",
         ]
 
         if filters_json:

clean_scripts/use_case_2_async_submission.py

@@ -58,22 +58,30 @@ def generate_target_settings(
     binder_length: int = 130,
     num_designs: int = 3
 ) -> Dict[str, Any]:
-    """Generate target settings JSON for BindCraft."""
+    """Generate target settings JSON for BindCraft in correct format.
+
+    Returns settings in the format expected by run_bindcraft.py:
+    - design_path: Output directory for designed binders
+    - binder_name: Prefix name for designed binders
+    - starting_pdb: Target protein PDB structure
+    - chains: Target chain(s) to design binder against
+    - target_hotspot_residues: Residue numbers to target (comma-separated)
+    - lengths: [min_length, max_length] range for binder length
+    - number_of_final_designs: Target number of accepted designs
+    """
     target_pdb_abs = resolve_path(target_pdb)
     output_dir_abs = resolve_path(output_dir)
 
     settings = {
-        "target_pdb": target_pdb_abs,
-        "target_chains": chains,
+        "design_path": output_dir_abs,                    # NOT "output_dir"
         "binder_name": name,
-        "binder_length": binder_length,
-        "num_designs": num_designs,
-        "output_dir": output_dir_abs,
+        "starting_pdb": target_pdb_abs,                   # NOT "target_pdb"
+        "chains": chains,                                  # NOT "target_chains"
+        "target_hotspot_residues": hotspot if hotspot else "",  # NOT "hotspot"
+        "lengths": [binder_length, binder_length],        # Array format, NOT single int
+        "number_of_final_designs": num_designs            # NOT "num_designs"
     }
 
-    if hotspot:
-        settings["hotspot"] = hotspot
-
     return settings
 
 
@@ -137,14 +145,17 @@ def run_async_submission(
         settings_file = output_dir / "target_settings.json"
         save_json(target_settings, settings_file)
 
+        # Get absolute path to settings file
+        settings_file_abs = str(settings_file.resolve())
+
         # Prepare command
         filters_json = defaults["filters"] if final_config["filters_enabled"] else None
         advanced_json = defaults["advanced"]
 
         cmd = [
             sys.executable,
             str(bindcraft_path / "run_bindcraft.py"),
-            f"--settings={settings_file}",
+            f"--settings={settings_file_abs}",
         ]
 
         if filters_json:

clean_scripts/use_case_4_batch_design.py

@@ -77,22 +77,30 @@ def generate_target_settings(
     binder_length: int = 130,
     num_designs: int = 2
 ) -> Dict[str, Any]:
-    """Generate target settings JSON for BindCraft."""
+    """Generate target settings JSON for BindCraft in correct format.
+
+    Returns settings in the format expected by run_bindcraft.py:
+    - design_path: Output directory for designed binders
+    - binder_name: Prefix name for designed binders
+    - starting_pdb: Target protein PDB structure
+    - chains: Target chain(s) to design binder against
+    - target_hotspot_residues: Residue numbers to target (comma-separated)
+    - lengths: [min_length, max_length] range for binder length
+    - number_of_final_designs: Target number of accepted designs
+    """
     target_pdb_abs = resolve_path(target_pdb)
     output_dir_abs = resolve_path(output_dir)
 
     settings = {
-        "target_pdb": target_pdb_abs,
-        "target_chains": chains,
+        "design_path": output_dir_abs,                    # NOT "output_dir"
         "binder_name": name,
-        "binder_length": binder_length,
-        "num_designs": num_designs,
-        "output_dir": output_dir_abs,
+        "starting_pdb": target_pdb_abs,                   # NOT "target_pdb"
+        "chains": chains,                                  # NOT "target_chains"
+        "target_hotspot_residues": hotspot if hotspot else "",  # NOT "hotspot"
+        "lengths": [binder_length, binder_length],        # Array format, NOT single int
+        "number_of_final_designs": num_designs            # NOT "num_designs"
     }
 
-    if hotspot:
-        settings["hotspot"] = hotspot
-
     return settings
 
 
@@ -127,14 +135,17 @@ def submit_single_job(
         settings_file = job_output_dir / "target_settings.json"
         save_json(target_settings, settings_file)
 
+        # Get absolute path to settings file
+        settings_file_abs = str(settings_file.resolve())
+
         # Prepare command
         filters_json = defaults["filters"] if config["filters_enabled"] else None
         advanced_json = defaults["advanced"]
 
         cmd = [
             sys.executable,
             str(bindcraft_path / "run_bindcraft.py"),
-            f"--settings={settings_file}",
+            f"--settings={settings_file_abs}",
         ]
 
         if filters_json: